From: Mo Chen (mochen.mmm_at_gmail.com)
Date: Fri May 30 2014 - 19:39:31 CDT
Sorry I did not paste the GROMACS part successfully and here it is.
[image: Inline image 2]
On Fri, May 30, 2014 at 5:35 PM, Mo Chen <mochen.mmm_at_gmail.com> wrote:
> Dear NAMD developers,
> I have a question about how NAMD calculate electrostatic energy.
> As cited from NAMD Guide 7.3.4:
> "In this scheme, the total force acting on each atom is broken into two
> pieces, a quickly varying local component and a slower long range
> component. The local force component is
> defined in terms of a splitting function. The local force component
> consists of all bonded and van der Waals interactions as well as that
> portion of electrostatic interactions for pairs that are separated by less
> than the local interaction distance determined by the splitting function.
> The long range component consists only of electrostatic interactions
> outside of the local interaction distance."
> Does this mean that in NAMD when using PME, the electrostatic energy
> within cutoff is the coulomb potential and the electrostatic energy outside
> cutoff is the long-range term calculated by PME? If so, there seems to be a
> little difference in calculating the short-range term between NAMD and
> GROMACS. Below is the short-range potential in GROMACS.
> May I ask if using the two slightly different methods for short-range
> electrostatic energy would result in significant deviations over long MD
> simulations? Thank you very much.
> Best regards,
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:26 CST